July 29, 2009

Demographic history of African farmers and hunters (Cox et al. 2009)

From the paper:

Median times since the onset of population growth are 1,863 (513–6,625), 1,027 (97–6,656), and 901 (38–6,497) generations ago, for the San, Biaka and Mandenka, respectively. Given a generation interval of 28 years [21], these values correspond to chronological dates of 52, 29 and 25 thousand years ago (or 37, 21 and 18 kya if we assume a 20-year generation interval). We obtain similar results with our larger Yoruban dataset. We infer a growth rate of 1.7×10−4 per generation (4.3×10−6–6.6×10−2), and a time of onset of growth at 1,280 (28–6,780) generations ago (or 36 kya), and 5-fold growth from ancestral size (Table 2)

...

The data from the three surveyed non-African populations (French Basque, Chinese Han, and Melanesians) are inconsistent with the simple growth model, presumably because they reflect more complex demographic histories. In contrast, data from all four sub-Saharan African populations fit the two-phase growth model, and a range of onset times and growth rates is inferred for each population. Interestingly, both hunter-gatherers (San and Biaka) and food-producers (Mandenka and Yorubans) best fit models with population growth beginning in the Late Pleistocene.

I am very doubtful of low-level exponential growth sustained over hundreds of generations, very doubtful that modern-day human gene pools contain a strong enough signal of past demographic history, and very doubtful that the demography of Eurasians is more complex than that of Africans. The paper could probably be improved by taking into account admixture processes in Africa itself, i.e., the fact that both African farmers and hunter-gatherers are the result of fairly recent admixture events, with introgressing of "farmer" genes in both San and Pygmies being particularly important.

The observed difference in inferred demography for Eurasians and Africans certaintly means something, but it's hard to evaluate how strong the case is for the scenario proposed in this paper.

UPDATE: The authors consider a simple 2-way admixture model for either recent cryptic admixture, or the Bantu expansion (3kya):

In the presence of gene flow or admixture (or a combination of both), our inference methods would tend to overestimate the effects of population growth, thus leading us to infer slightly older and stronger growth than actually occurred.

But, what about more ancient admixture? The recent Tishkoff et al. paper suggests substantial structure and admixture in African populations that goes well beyond a simple Bantu+Hunter-gatherer model. Even clusters that appear to be homogeneous in that study may reflect stabilized blends of earlier admixture events. If Europeans came into contact with Africans after Pygmies and San had disappeared (as seems likely to happen eventually), we would not even know that such peoples ever existed. How many more small hunter groups were absorbed by expanding African populations (pre-Neolithic or Neolithic), leaving no trace today?

Unlike the authors, I think Eurasian demography is fairly simple in comparison to the African one. There is nothing metaphysical about this guess: Africa, being the cradle of Homo sapiens, is likely to have had the largest human populations, for the longest time. These populations did not sit idly for so long, waiting to be discovered by outsiders, but experienced growth, admixture, competition leading to extinction or absorption, etc.

PLoS ONE 4(7): e6366. doi:10.1371/journal.pone.0006366

Autosomal Resequence Data Reveal Late Stone Age Signals of Population Expansion in Sub-Saharan African Foraging and Farming Populations

Murray P. Cox et al.

Abstract

Background

A major unanswered question in the evolution of Homo sapiens is when anatomically modern human populations began to expand: was demographic growth associated with the invention of particular technologies or behavioral innovations by hunter-gatherers in the Late Pleistocene, or with the acquisition of farming in the Neolithic?

Methodology/Principal Findings

We investigate the timing of human population expansion by performing a multilocus analysis of≥20 unlinked autosomal noncoding regions, each consisting of ~6 kilobases, resequenced in ~184 individuals from 7 human populations. We test the hypothesis that the autosomal polymorphism data fit a simple two-phase growth model, and when the hypothesis is not rejected, we fit parameters of this model to our data using approximate Bayesian computation.

Conclusions/Significance

The data from the three surveyed non-African populations (French Basque, Chinese Han, and Melanesians) are inconsistent with the simple growth model, presumably because they reflect more complex demographic histories. In contrast, data from all four sub-Saharan African populations fit the two-phase growth model, and a range of onset times and growth rates is inferred for each population. Interestingly, both hunter-gatherers (San and Biaka) and food-producers (Mandenka and Yorubans) best fit models with population growth beginning in the Late Pleistocene. Moreover, our hunter-gatherer populations show a tendency towards slightly older and stronger growth (~41 thousand years ago, ~13-fold) than our food-producing populations (~31 thousand years ago, ~7-fold). These dates are concurrent with the appearance of the Late Stone Age in Africa, supporting the hypothesis that population growth played a significant role in the evolution of Late Pleistocene human cultures.

2 comments:

I recall that when Trevor Jenkins and George Nurse did the genetics tests on my blood samples from Botswana in 1978, from sample that was half San and half BaKgalahadi (Bantu-speaking) from the Northern Kweneng area, just south of the Central Kalahari Game reserve, they could not readily distinguish between the two samples. Helga Vierich

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